Small research and development activity
project / Applying wheat quality markers in India
project number / CIM/2010/014
date published / April 2011
prepared by / Dr Howard Eagles
contributors/ collaborators / Dr Karen Cane
approved by / Dr Paul Fox
final report number / FR2011-06
ISBN / 978 1 921738 60 9
published by / ACIAR
GPO Box 1571
Canberra ACT 2601
Australia
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© Australian Centre for International Agricultural Research (ACIAR) 2011 - This work is copyright. Apart from any use as permitted under the Copyright Act 1968, no part may be reproduced by any process without prior written permission from ACIAR, GPO Box 1571, Canberra ACT 2601, Australia, .
Final report:
Contents
1 Acknowledgments 4
2 Executive summary 5
3 Introduction 6
4 Activities 7
4.1 Identification of Australian biscuit wheat cultivars to send to India 7
4.2 Identification and characterisation of the reference set 7
4.3 Coordination with CIM/2005/020 ‘Molecular marker technologies for faster wheat breeding in India’ 8
4.4 Presentations 8
4.5 Important meetings 9
4.6 Cross prediction and ICIS 9
4.7 Germplasm of potential value in Australia 10
5 Conclusions and recommendations 11
5.1 Conclusions 11
5.2 Recommendations 11
6 References 12
6.1 References cited in report 12
6.2 List of publications produced by project 12
7 Appendix 13
Page 13
Final report:
1 Acknowledgments
Dr Anju Mahendru Singh, for organising the documentation for the import of Australian biscuit cultivars into India, the distribution of seed, and the cultivation of the 5 biscuit cultivars in the 2009/10 rabi season at IARI. Her encouragement and interest in the reference set activity is also appreciated. Dr G.P. Singh of IARI and Dr Navtaj Bains of Punjab Agricultural University for their interest and stimulating discussions on plant breeding aspects of the project.
We acknowledge the advice of Dr Marie Appelbee of LongReach Plant Breeders, Dr Russell Eastwood of Australian Grain Technologies and Dr Robyn McLean of InterGrain on appropriate cultivars to send to India. Dr Appelbee also assisted with the molecular characterisation of the Australian biscuit cultivars, and Indian cultivars in the reference set for glutenin genes.
We also acknowledge the assistance of Prof Richard Trethowan, Dr Harbans Bariana and Dr Urmil Bansal for advice on travel in India and stimulating scientific discussions while travelling in India. Prof Trethowan was particularly helpful in providing seed of Indian cultivars in the reference set.
Dr Paul Fox of ACIAR in facilitating interactions between Indian collaborators and the Australian research team and through funding and participation at the ICIS workshop and Karnal meetings. Dr Kuhu Chatterjee and Ms Simrat Labiana for assisting with many aspects of our visits to India.
2 Executive summary
Biscuits are widely consumed in India, but elite biscuit quality cultivars are not available to Indian farmers or industry. Australia has elite biscuit cultivars and extensive knowledge of many of the genes required for elite biscuit quality. Specific alleles of both glutenin and puroindoline genes are required and these can be identified by diagnostic molecular markers. This provides the opportunity to establish a breeding program with the immediate objective of developing biscuit cultivars, but also, in the longer term, as a model for integrating cross prediction technologies based on molecular markers into Indian wheat breeding.
Five elite Australian biscuit cultivars, Barham, Yenda, EGA Jitarning, EGA 2248 and Orion were identified and exported to India. These were characterised for 24 genes, including those known to be required for biscuit quality, adaptation and disease resistance. A further fourteen Australian cultivars, known to already be available in India, and 15 diverse Indian cultivars were also characterised for the same 24 genes. In collaboration with Prof Richard Trethowan, these characterisations were entered into the ICIS database which is being used by Indian wheat breeders. Importantly, this characterisation of 34 cultivars for 24 genes made a reference set that could be used to facilitate the use of molecular markers in Indian wheat breeding programs.
Protocols were written to assist with the use of these markers. Already, requests have been made through the Generation Challenge Program for these marker protocols to be distributed more widely than just to the participants of this SRA. We recommend that approval be given for their wider distribution.
Diagnostic markers for grain quality and adaptation were used to predict the outcome of crossing cultivars like Yenda with Indian cultivars adapted to north-western India. We concluded that marker-based selection among BC1F1 plants would greatly improve the frequency of desirable progeny from these crosses. This methodology was discussed with Dr G.P. Singh, who plans to continue with the development of biscuit cultivars in India. His colleague, Dr Mahendru Singh, has the equipment and skills required for the completion of this project, so long as it remains a priority for Indian wheat breeding. We therefore concluded that there were no grounds to continue this SRA with a larger project.
3 Introduction
Biscuits are widely consumed in India, but elite biscuit quality cultivars are not available to Indian farmers or industry. Australia has elite biscuit cultivars that are expected to perform in India at levels below current elite cultivars, but at levels beyond those of landraces and many other potential sources of genes needed to develop biscuit cultivars adapted to Indian conditions. Furthermore, from extensive research, a great deal is known about the genetic basis of biscuit quality in Australia. This provides the opportunity to use the establishment of a breeding program for biscuit cultivars to be used for the immediate purpose of developing biscuit cultivars, but also, in the longer term, as a model for integrating cross prediction technologies into Indian wheat breeding.
Activities in this SRA fell into three broad areas:
1. The identification and transfer to India of elite Australian biscuit wheat cultivars that could be used as parents in the breeding of biscuit cultivars adapted to Indian conditions.
2. The identification of a reference set of Indian and Australian cultivars that could subsequently be characterised with diagnostic markers for genes controlling grain quality, phenology, disease resistance and tolerance of abiotic stresses. These characterisations could then be used as controls for Indian molecular scientists associated with breeding programs to use in Indian wheat breeding programs, just as they are in Australian programs. They would also be valuable for future collaboration between India and Australia in molecular wheat breeding.
3. To work with Indian wheat breeders on useful strategies for using molecular markers for designing crosses for developing biscuit cultivars, but with the longer-term objective of the wider use of markers for all classes of wheat. This activity overlapped substantially with activities in CIM/2005/020 ‘Molecular marker technologies for faster wheat breeding in India’, led by Prof Richard Trethowan.
4 Activities
4.1 Identification of Australian biscuit wheat cultivars to send to India
After consultation with Dr Russell Eastwood, AGT, Dr Robyn McLean, InterGrain, and Dr Marie Appelbee, LongReach, all successful Australian breeders of biscuit cultivars, the following elite cultivars were identified:
· Barham
· Yenda
· EGA Jitarning
· EGA 2248
· Orion
As indicated from the pedigrees in ICIS, these cultivars are not closely related. All are suitable for the Australian Soft class, but, in addition, some of these cultivars carry genes for tolerance to abiotic stresses and resistance to diseases that should be useful to Indian wheat breeders beyond their value as donors of genes for biscuit quality. For example, Yenda was known to carry the Bo1 gene for tolerance to high levels of boron and the Rlnn1 gene for resistance to root lesion nematodes. These characteristics were considered in the selection of these cultivars.
Through correspondence with Dr Mahendru Singh, importation permits for India were obtained and pure seed of the cultivars was sent from the Australian Winter Cereals Collection to India on 24 September 2010, in time for the coming rabi season. Subsequently, Drs Cane and Eagles observed the cultivars being successfully grown at IARI in Delhi on 18 February 2011, with crosses already being made to selected Indian cultivars. Dr Eagles was pleasantly surprised to find that these Australian cultivars were flowering almost simultaneously with adapted Indian cultivars, which augurs well for their use in Indian wheat breeding.
4.2 Identification and characterisation of the reference set
At a meeting on 11 September, 2010, in Karnal a set of 15 Indian cultivars were identified for use in a reference set. This meeting was chaired by Dr S.S. Singh. These cultivars were selected to represent diversity of Indian germplasm and to be complementary to Australian cultivars already in India. They included both modern and older cultivars. In addition, 19 diverse Australian cultivars were identified. Seed of the Australian cultivars had to already be in India, and were also chosen for their known diversity. The five biscuit cultivars were included.
At this meeting, genes with diagnostic markers of interest to both Indian and Australian wheat breeders were identified.
The final set included the following genes affecting grain quality:
Glu-A1, Glu-B1, Glu-D1, Glu-A3, Glu-B3, Glu-D3, Pina-D1, Pinb-D1, Srp5B, Spa-A1, Spa-B1, Spa-D1
The final set included the following genes affecting plant phenology, morphology and disease resistance:
Ppd-D1, Vrn-A1, Vrn-B1, Vrn-D1, Rht-B1, Rht-D1, VPM-1, Sr24/Lr24, Lr34/Yr18, Sr2, Tsn1, Sr26
Seed of the selected Indian cultivars was obtained in Australia from Prof. Trethowan. In the laboratory of Dr Karen Cane, the full reference was characterised for the above genes. These results were sent to India in detailed spreadsheets, with copies also sent to Dr Paul Fox at ACIAR. Our Indian colleagues characterised genes and cultivars of interest, for example Dr Sewa Ram at DWR in Karnal was especially interested in Spa genes, as potentially involved in determining chapati quality.
There were some unexpected findings. One was the far higher frequency of the resistant (null) allele of Tsn1, which contributes to resistance to nectrotrophic diseases, in Indian compared to Australia cultivars. This will be investigated further by Prof Trethowan in CIM/2005/020. The second was the finding of variation in Spa-A1 and Spa-D1 in Indian, but not Australian cultivars. This will be investigated further by Dr Sewa Ram.
Detailed protocols were written by Dr Cane and distributed for many of these genes. As will be discussed later, the Generation Challenge Program has expressed an interest in distributing these protocols more widely than was anticipated in this project.
Ppd-B1 was added in Australia, but as these protocols were obtained in confidence from the John Innes Centre in the UK, no results were shared with our Indian colleagues. These will be distributed if approval is obtained from the John Innes Centre in a reasonable period of time.
4.3 Coordination with CIM/2005/020 ‘Molecular marker technologies for faster wheat breeding in India’
Activities in this project were closely coordinated with those in CIM/2005/020. Dr Eagles attended the ICIS workshop from 13 to 16 September 2010 in Delhi and Drs Eagles and Cane travelled with Prof Trethowan, Dr Bariana and Dr Brettell in February 2011 and contributed to Dr Brettell’s review of CIM/2005/020. During February, Dr Eagles observed the successful use of ICIS in breeding programs in India, in both the GMS (Genealogical Management System) and DMS (Data Management System). This was especially true for the program at Punjab Agricultural University led by Dr Bains.
Prof Trethowan entered the marker results into the ICIS database for subsequent use in both India and Australia.
As relevant pedigrees were identified, these were sent to Prof Trethowan and Mr Manoj Singh for entry into ICIS.
4.4 Presentations
The following presentations were made during this SRA:
Howard Eagles and Karen Cane. Using Diagnostic Markers and Cross Prediction. 15 September 2010, Delhi. Full seminar.
Howard Eagles and Karen Cane. Using Diagnostic Markers and Cross Prediction. SRA: Applying wheat quality markers in India. 6 October 2010, Adelaide. Short presentation. In this presentation plans for the SRA were presented and accomplishments during the first 3 months were described.
Howard Eagles and Karen Cane. Using Diagnostic Markers and Cross Prediction. SRA: Applying wheat quality markers in India. 16 February 2011, Karnal. Short presentation. In this presentation accomplishments of the SRA were described and discussed, especially how the reference set activity could be used in Indian wheat breeding and how Indian wheat breeders should consider the effects of winter alleles of the Vrn-A1 gene (Eagles et al. 2011) on the performance of their most important cultivars.
Howard Eagles. Association Genetics, ICIS, and Cross Prediction. 30 March 2011, Hyderabad. Full seminar. In this presentation the association genetics approach used in our research was described with emphasis on how ICIS was essential for predictions with minimal bias. The CrossPredictor software developed by the Molecular Plant Breeding CRC was described and the incorporation of similar functionality in future plant breeding software was advocated.
4.5 Important meetings
On 11 September 2010 Dr Cane visited the laboratories of Dr Ratan Tiwari at DWR in Karnal. She concluded that the laboratories in Karnal possessed all the equipment necessary to complete the molecular analysis proposed in this SRA. Advice was offered on the interpretation of molecular marker results already obtained in the laboratory and a short presentation on specific diagnostic marker protocols was given by Dr Cane to Dr Tiwari, research staff and graduate students.
On 15 September 2010 Dr Cane visited the laboratories of Dr Mahendru Singh at IARI; the laboratory capabilities were reviewed and found to be highly satisfactory for the purposes of this project. A short presentation on specific diagnostic marker protocols was presented to Dr Mahendru Singh and her assistant Mr Santosh Singh, who would be responsible for the molecular analysis
On 18 February 2011 discussions were held among Dr Anju Mahendru Singh, Dr G.P. Singh, Dr Karen Cane and Dr Howard Eagles at IARI in Delhi. During these meetings we reached the following important conclusions: